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Experimental evidence for evolution

Discussion of everything related to the Theory of Evolution.

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Re: Experimental evidence for evolution

Postby robsabba » Mon Jun 21, 2010 4:20 pm

jevg wrote:The Long Term Evolution Experiment (LTEE) has been going on since 1988.

http://www.pnas.org/content/105/23/7899.full.pdf+html


By way of some background, Evolutionists debate a lot about how evolution works. Stephen Jay Gould suggested that sometimes mutations happen that have no immediate benefit; but those mutations remain in the gene pool because they are not harmful. Those mutations are just floating in the gene pool waiting to be used. Then a subsequent mutation that depends upon those previous mutations can occur that causes some benefit to the organism. In other words, a new mutation might depend upon other mutations that happened in the past. Scientists call this, “historical contingency.” “Historical contingency” simply means, “it depends upon something that happened in the past.”

Gould’s opponents say that the environment drives evolution to a particular solution, so it doesn’t depend on past accidents. Furthermore, a mutation that has no immediate benefit will likely disappear from the gene pool before it is eventually needed

The Experiment

They started out with 12 individual, identical E. coli bacteria and put each one in its own little Petri dish; and they grew into 12 colonies.
E. coli bacteria reproduce asexually. In simple terms, the bacteria grow bigger and bigger until they get large enough to split in half, so the parent cell turns into two identical child cells.. Although the division process nearly always produces two identical children, sometimes the process partially fails, producing mutant offspring.
It takes nearly 2 hours for E. coli bacteria to reproduce, so there are about 6.5 generations born every day. This is convenient for scientists because it allows them to study lots of generations in a reasonable amount of time.
So, if you start out with 1 bacterium, you will have 2 in about 2 hours, then 4 two hours later, then 8 two hours after that, then 16, then 32, then 64, and finally 128 in just over a day. It is very convenient that the colony grows by a factor of roughly 100 every day.

They fed them glucose and citrate, and gave them 12.2 times more citrate than glucose. This was critical because E. coli can’t digest citrate.. E. coli would die on a steady diet of citrate.

The goal of the experiment was to try to force the E. coli to evolve in such a way that they could digest citrate, like some other bacteria can.

They did this by giving the bacteria just enough glucose to keep them alive, and an abundance of citrate. The expectation was that if the E. coli did evolve into a form that could digest citrate, that new variety would flourish in the citrate-rich environment and drive the old variation to extinction.

One important caveat is this.
If you read the fine print, you will discover that E. coli can ALMOST digest citrate.

Result

It took more than 30,000 generations to fully evolve a capability that was already almost there, and it only happened in 1 out of 12 populations.

Thirty-thousand generations isn’t a long time for a bacterium, but 30,000 generations for people is about 600,000 years.

They really had to try hard using all the evolutionary pressure they could muster, to produce this minimal change.

However there was one unexpected result from this experiment.

QUOTE from the paper

The origin of the Cit+ function also had profound consequences for the ecology and subsequent evolution of that population. This new capacity was refined over the next 2,000 generations, leading to a massive population expansion as the Cit+ cells evolved to exploit more efficiently the abundant citrate in their environment. Although the Cit+ cells continued to use glucose, they did not drive the Cit– subpopulation extinct because the Cit– cells were superior competitors for glucose. Thus, the overall diversity increased as one population gave rise evolutionarily to an ecological community with two members, one a resource specialist and the other a generalist.


One of the fundamental ideas behind the theory of Darwinian evolution is extinction. Natural selection allows the group that is more fit for survival to drive the less fit ancestors to extinction.
In this experiment, the new variety did not drive the old variety to extinction.

Presumably that is because there was enough food for both varieties. Hasn’t there always been enough food for just one transitional form to survive, at least long enough to leave some fossils?
The primary thing we learn from this experiment is how difficult it is to cause even the smallest amount of evolution.

The LTEE showed that after 20 years of extreme, relentless pressure, it is possible for a minimal improvement in digestion to occur (after just 30,000 generations ).

How many generations it would take to develop a whole digestive tract from teeth to anus.?

The experiment is still continuing having reached about 50,000 generations with no additional results.

Creationists hate the Lenski experiments because it blows holes in some of their most beloved paradigms:
1. Natural selection cannot lead to an increase in "information."
2. Evolution cannot produce new functions.

Interesting that you refer to "relentless pressure," as if nature is not capable of producing such pressures. It is.

Evolution works with what is already there. An entirely new metabolic pathway is unlikely to evolve from scratch. Therefore your critiscism that E.coli can normally "almost" make use of citrate anyway makes little sense. The point is a new metabolic function evolved in a relatively short period of time. And no, 30,000 generations is not a long time evolutionarily speaking. How long would it take to evolve a digestive system? Obviously longer than 30,000 generations. No one has ever suggested differently.

While extinction is important for evolution, since it frees up ecological niches that were previosuly occupied, it is not necessary for macro-evolution. In fact, the fossil record shows that many different related species can co-exist at the same time and even in the same location. Examples include the ancestors of both man and the modern horse. Now lets look at the Lenski experiment again. What would happen if the supply of glucose was cut off? It would quickly lead to the extinction of the non-citrate capable population.

You claimed that nothing else happened in 50,000 generations. This is completely false. The paper you cited mentions other examples of evolution in the introduction, including: higher growth rates on glucose, shorter lag phases, reduced peak population densities, larger average size, increased DNA supercoiling, defects in DNA repair, and changes in many gene-expression profiles. In fact, there are more than a dozen papers previously published on this project that were cited in this paper. What did you think there were about? Nothing happening in 50,000 generations?
Last edited by robsabba on Mon Jun 21, 2010 4:28 pm, edited 2 times in total.
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Re:

Postby robsabba » Mon Jun 21, 2010 4:25 pm

jevg wrote:The Long Term Evolution Experiment (LTEE) has been going on since 1988.
Some more detail of terms of the experiment.

When I stated in my last post that E. coli can ALMOST digest citrate” this was deserving of a little more explaination.
E . coli already has a number of enzymes that normally use citrate and can digest it . However, it lacks an enzyme called a citrate permease which can transport citrate from outside the cell through the cell’s membrane into its interior. All that was needed therefore to use citrate, was to find a way to get it into the cell. The rest of the machinery for its metabolism was already there.
Lenski put it this way “The only known barrier to aerobic growth on citrate is its inability to transport citrate under oxic conditions.

The team have not been able to track down the mutation(s), however the point that the paper emphasizes is the historical contingency of the new capability. The evidence shows that in only one of the 12 population lines, and after some 20,000 generations a “potential” ( potentiating mutation) occurred that allowed at least a second mutation after 30,000 generations to give rise to the new citric capability.

So Richard Lenski is affirming that the evolution of some pretty simple cellular features likely requires multiple mutations.

If the development of many of the features of the cell required multiple mutations during the course of evolution, as this continuing experiment suggests, then this is another reason why Darwinian theory does not provide the answers to cell development.

How does the fact that historical contingency DOES work in an actual evolutionary scenario provide evidence that "Darwinian theory does not provide the answers to cell development?"
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Re: Experimental evidence for evolution

Postby jevg » Tue Jun 22, 2010 9:58 pm

Hi robsabba
Thanks for your comments.
My response is as follows
Creationists hate the Lenski experiments because it blows holes in some of their most beloved paradigms:
1. Natural selection cannot lead to an increase in "information."
2. Evolution cannot produce new functions.

As I am neither a creationist nor any other “ist” I’m afraid this comment of yours escapes me.

Therefore your critiscism that E.coli can normally "almost" make use of citrate anyway makes little sense.


That E.coli can normally "almost" make use of citrate is not a critiscism.
It was simply stated as a fact and I am at a loss to understand how you could regard that as a critisism. I was only stating what Lenski was himself was reporting albeit I did paraphase it somewhat. However as you will note I clarified that “almost” bit in my second posting.

The point is a new metabolic function evolved in a relatively short period of time.


Actually no new metabolic function evolved. Please read the paper carefully.

The ability to digest citrate was already there. What was lacking was the ability to transport the citrate from the outside environment through the cell membrane into the interior.
This is how Lenski himself reports it in the paper
“The only known barrier to aerobic growth on citrate is its inability to transport citrate under oxic conditions” (para 5)

How did that capability come about? Well Lenski has been unable to identify the cause.
He refers to a few possible causes in para 5 & 6.

Indeed, atypical E. coli that grow aerobically on citrate (Cit_) have been isolated from agricultural and clinical settings, and were found to harbor plasmids, presumably acquired from other species, that encode citrate transporters (44, 45).
Other findings suggest that E. coli has the potential to evolve a Cit_ phenotype. Hall (41) reported the only documented case of a spontaneous Cit_ mutant in E. coli. He hypothesized that some complex mutation, or multiple mutations, activated cryptic genes that jointly expressed a citrate transporter, although the genes were not identified.
Pos et al. (43) identified an operon in E. coli K-12 that apparently allows anaerobic citrate fermentation, and which includes a gene, citT, encoding a citrate– succinate antiporter. High-level constitutive expression of this gene on a multicopy plasmid allows aerobic growth on citrate, but the native operon has a single copy that is presumably induced only under anoxic conditions.


Please note my emphasis on the uncertainty he and others have expressed

However Lenski himself continues with this finding (para 7)

"Despite this potential, none of the 12 LTEE populations evolved the capacity to use the citrate that was present in their environment for over 30,000 generations. During that time, each population experienced billions of mutations (22), far more than the number of possible point mutations in the _4.6-million-bp genome. This ratio implies, to a first approximation, that each population tried every typical one-step mutation many times. It must be difficult, therefore, to evolve the Cit_ phenotype, despite the ecological opportunity"

According to standard evolutionary theory, every adaptation, even the most sophisticated, is the product of a series of simple adaptive steps. Adaptive steps are thought typically to involve a single mutation, though steps requiring two independent mutations may also be feasible under some circumstances. Whether by single mutations or double mutations, though, as long as each step of an adaptive path is both feasible and beneficial, it is commonly assumed that the path will be followed

The point that Lenski is making in part of the quote I have emphasised and underlined above, is that this experiment suggests that the common assumption of the standard (Darwinian) theory of successive one step mutations providing function isn’t being borne out in his experiment.

This is the reason why he is suggesting that this experiment favours Gould’s Historical Contingency proposal rather than the standard Darwinian explanation.

If you research the history of Gould’s and Eldridge’s theory of Punctuated Equilibrium you will appreciate why they are so controversial among some prominent evolutionary scientists.

Punctuated Equilibrium is a theory that does not agree with Darwinian explanation

I hope this also answers your last question in your second post quoted below
How does the fact that historical contingency DOES work in an actual evolutionary scenario provide evidence that "Darwinian theory does not provide the answers to cell development?"


I’m a little bit tied for time to respond to your other comments but will do so very shortly
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Re: Experimental evidence for evolution

Postby kamyar » Wed Jun 23, 2010 2:11 am

Hi
has anyone done a computer model/simulation of evolution?
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Re: Experimental evidence for evolution

Postby canalon » Wed Jun 23, 2010 2:53 am

jevg wrote:
According to standard evolutionary theory, every adaptation, even the most sophisticated, is the product of a series of simple adaptive steps. Adaptive steps are thought typically to involve a single mutation, though steps requiring two independent mutations may also be feasible under some circumstances. Whether by single mutations or double mutations, though, as long as each step of an adaptive path is both feasible and beneficial, it is commonly assumed that the path will be followed

The point that Lenski is making in part of the quote I have emphasized and underlined above, is that this experiment suggests that the common assumption of the standard (Darwinian) theory of successive one step mutations providing function isn’t being borne out in his experiment.


Here is the problem. Evolution, as we now see it includes point mutation, but it is far from the only source of novelty in genomes. Horizontal gene transfer (multiple mechanism involved) and gene duplication are also essential to the ability to evolve new genes. From this point of view, the Lenski experiment is overly simplistic as there are very limited possibility of exchange of genes in his populations :
-They are maintained in exponential growth: no dead cells to scavenge
-Absence of phages
-Absence of other bacteria that can act both as donor for new genes and also as a way to accelerate intraspecific gene exchange
-Limited environmental stress that could affect the genome (ie: UV)

So yeah it is far from being a true reflection of all that could drive evolution, but hey, you have to start somewhere, and this is a darn good one. And that demonstrate that creation of a gene de novo is probably not a very frequent event.
And as far as I understand it, the historical contingency is definitely a huge part of the evolution as it is now accepted, and was already part of Darwin's understanding, even if he did not emphasize it in the the origin of species. Granted, my lecture of it was probably contaminated by my knowledge of recent biology, but it does not seem that Gould was revolutionary on this respect.
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Re: Experimental evidence for evolution

Postby robsabba » Wed Jun 23, 2010 2:25 pm

jevg wrote:Hi robsabba
Thanks for your comments.
My response is as follows
Creationists hate the Lenski experiments because it blows holes in some of their most beloved paradigms:
1. Natural selection cannot lead to an increase in "information."
2. Evolution cannot produce new functions.

As I am neither a creationist nor any other “ist” I’m afraid this comment of yours escapes me.

Therefore your critiscism that E.coli can normally "almost" make use of citrate anyway makes little sense.


That E.coli can normally "almost" make use of citrate is not a critiscism.
It was simply stated as a fact and I am at a loss to understand how you could regard that as a critisism. I was only stating what Lenski was himself was reporting albeit I did paraphase it somewhat. However as you will note I clarified that “almost” bit in my second posting.

The point is a new metabolic function evolved in a relatively short period of time.


Actually no new metabolic function evolved. Please read the paper carefully.

The ability to digest citrate was already there. What was lacking was the ability to transport the citrate from the outside environment through the cell membrane into the interior.
This is how Lenski himself reports it in the paper
“The only known barrier to aerobic growth on citrate is its inability to transport citrate under oxic conditions” (para 5)

How did that capability come about? Well Lenski has been unable to identify the cause.
He refers to a few possible causes in para 5 & 6.

Indeed, atypical E. coli that grow aerobically on citrate (Cit_) have been isolated from agricultural and clinical settings, and were found to harbor plasmids, presumably acquired from other species, that encode citrate transporters (44, 45).
Other findings suggest that E. coli has the potential to evolve a Cit_ phenotype. Hall (41) reported the only documented case of a spontaneous Cit_ mutant in E. coli. He hypothesized that some complex mutation, or multiple mutations, activated cryptic genes that jointly expressed a citrate transporter, although the genes were not identified.
Pos et al. (43) identified an operon in E. coli K-12 that apparently allows anaerobic citrate fermentation, and which includes a gene, citT, encoding a citrate– succinate antiporter. High-level constitutive expression of this gene on a multicopy plasmid allows aerobic growth on citrate, but the native operon has a single copy that is presumably induced only under anoxic conditions.


Please note my emphasis on the uncertainty he and others have expressed

However Lenski himself continues with this finding (para 7)

"Despite this potential, none of the 12 LTEE populations evolved the capacity to use the citrate that was present in their environment for over 30,000 generations. During that time, each population experienced billions of mutations (22), far more than the number of possible point mutations in the _4.6-million-bp genome. This ratio implies, to a first approximation, that each population tried every typical one-step mutation many times. It must be difficult, therefore, to evolve the Cit_ phenotype, despite the ecological opportunity"

According to standard evolutionary theory, every adaptation, even the most sophisticated, is the product of a series of simple adaptive steps. Adaptive steps are thought typically to involve a single mutation, though steps requiring two independent mutations may also be feasible under some circumstances. Whether by single mutations or double mutations, though, as long as each step of an adaptive path is both feasible and beneficial, it is commonly assumed that the path will be followed

The point that Lenski is making in part of the quote I have emphasised and underlined above, is that this experiment suggests that the common assumption of the standard (Darwinian) theory of successive one step mutations providing function isn’t being borne out in his experiment.

This is the reason why he is suggesting that this experiment favours Gould’s Historical Contingency proposal rather than the standard Darwinian explanation.

If you research the history of Gould’s and Eldridge’s theory of Punctuated Equilibrium you will appreciate why they are so controversial among some prominent evolutionary scientists.

Punctuated Equilibrium is a theory that does not agree with Darwinian explanation

I hope this also answers your last question in your second post quoted below
How does the fact that historical contingency DOES work in an actual evolutionary scenario provide evidence that "Darwinian theory does not provide the answers to cell development?"


I’m a little bit tied for time to respond to your other comments but will do so very shortly

I included the ability to transport a molecule across a cell membrane as a "metabolic function." You can split hairs about that if you like, but the point is that these bacteria were now able to make use of a new carbon source that the ancestral population could not. As far as the rest is concerned, I may have misunderstood your use of the term "Darwinian." Many people use it interchangably with "evolutionary." It is hard nowadays to understand what people mean by the term. If you are specifically refering to classical evolution according to Darwin, then all I can say is that the science of evolutionary biology has advanced well past Darwin. In fact, Darwin knew nothing about where the variability that evolution works with actually comes from. He knew nothing about DNA or genes or mutations. You seem to be citing this parer in agreement with this conclusion. If so, I agree. Is that really your only point?
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Re: Experimental evidence for evolution

Postby jevg » Fri Jun 25, 2010 10:16 am

Hi robsabba
I included the ability to transport a molecule across a cell membrane as a "metabolic function." You can split hairs about that if you like, but the point is that these bacteria were now able to make use of a new carbon source that the ancestral population could not. As far as the rest is concerned, I may have misunderstood your use of the term "Darwinian." Many people use it interchangably with "evolutionary." It is hard nowadays to understand what people mean by the term. If you are specifically refering to classical evolution according to Darwin, then all I can say is that the science of evolutionary biology has advanced well past Darwin. In fact, Darwin knew nothing about where the variability that evolution works with actually comes from. He knew nothing about DNA or genes or mutations. You seem to be citing this parer in agreement with this conclusion. If so, I agree. Is that really your only point?


I don’t accept I was splitting hairs, - bringing meat to the table and digesting that meat are two different functions, the function that evolved in the Lenski experiment is the “bringing” bit. However we can agree to differ I’m sure,
When I use the expression Darwinian I am of course referring to the Modern synthesis or neo Darwinism as it is often known.
To avoid any further misunderstandings Let me firstly explain my current understanding.
Evolution is a fact. I don’t think anyone seriously argues that point.

The question that needs to be properly answered though is
“what are the limits, if any to what evolution can achieve”?



The fundamental tenets of the modern standard theory are random mutations of genetic material followed by natural selection operating on populations, the process is gradual and this drives towards speciation.(new species)
A central tenet being in the words of Simon Conway Morris “that evolution is for all intents and purposes open-ended and indeterminate in terms of predictable outcomes.”
A tenet incidentally that he actually disagrees with.
http://rstb.royalsocietypublishing.org/ ... 3.full.pdf

Eldridge and Gould argued that gradualism is not manifest in the fossil record as that shows rapid periods of evolution followed by long periods of stastis., hence Punctuated Equilibrium.
As canalon has noted, Darwin was aware of this privately but did not try to explain in his “Origin of Species” .His theory was based on gradualism and this gradualism has been retained in the modern synthesis.

Historical Contingency is a main driving mechanism according to Eldridge and Gould
As such it renders evolution fundamentally quirky and unpredictable and not repeatable.

According to Simon Conway Morriss however, evolution is broadly repeatable ( nearly non random) with contingency mostly confined to minor details.


This experiment is what good science is all about.
It is not relying on historical science but experimental science and therefore the data is dependable. What conclusions can be drawn from the results?

Lenski interprets the results in support of the Gould hypothesis, i.e. historical contingency

However Simon Conway Morris interprets these same results to support his understanding of
Evolutionary theory.

Michael Behe the articulator of the ID community interprets the results as supporting his view.
http://www.amazon.com/gp/blog/post/PLNK3U696N278Z93O

There are of course other opinions from eminent scientists
So who is right - is there a definitive answer?

In arguing his case Conway Morris puts it this way.
“That evolution is not utterly random is evident from the ubiquity of homoplasy, ( convergent evolution) at least within clades that encompass lower parts of the taxonomic hierarchy. The question, however, is does this principle extend to the major divisions of life? No definitive answer can yet be given, not least because the origins of the great majority of major groups are shrouded in obscurity, although jointly molecular data and the fossil record continue to make major assaults on this citadel of ignorance.”
In English – science doesn’t have an answer.

So why so much heat when someone dares to question standard theory?

I do find Morriss’s take on this really amusing.
“Yet, if evolution is glaringly obvious, why is it not only greeted with growing hostility, but the siren-call of anti-evolutionary dogma, notably ‘intelligent design’, remains a rallying point to individuals that in any other respect fail to manifest any obvious sign of mental instability? :)
The reasons, of course, are complex and so far as the explication (and defence) of the science of evolution is concerned, it can hardly be assisted by those who ironically treat it as a religion (Midgley 1985).” :)

The fact is science does not have an answer to the origin of speciation

So as I see matters the original question of this thread “whether there have been any experiments conducted that provide empirical support for macroevolution.”
As yet no

Lenksi’s experiment is probably the most extensive yet and after over 20years of selective pressure over some 360,000 generations ( 12 x 30,000) has produced a minor novel trait.

However canalon has quite reasonably pointed out that the growth environment is somewhat simplistic, as it does not compare in wild nature. But this is a good start.


Here is some more food for thought

http://www.bioone.org/doi/abs/10.1095/b ... 104.031302
some more information here
http://findarticles.com/p/articles/mi_m ... n13595924/
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Re: Experimental evidence for evolution

Postby canalon » Fri Jun 25, 2010 3:43 pm

jevg wrote:Eldridge and Gould argued that gradualism is not manifest in the fossil record as that shows rapid periods of evolution followed by long periods of stasis, hence Punctuated Equilibrium.
As canalon has noted, Darwin was aware of this privately but did not try to explain in his “Origin of Species” .His theory was based on gradualism and this gradualism has been retained in the modern synthesis.

Historical Contingency is a main driving mechanism according to Eldridge and Gould
As such it renders evolution fundamentally quirky and unpredictable and not repeatable.

According to Simon Conway Morris however, evolution is broadly repeatable ( nearly non random) with contingency mostly confined to minor details.


Attention, I did not say that. What I said is that historical contingency was tacit in the Origin of Species, at least when I read it, but certainly not punctuated equilibrium. Which is a definitely new evolution (pun intended) of the theory brought by Gould and Eldridge. I do not think that Darwin was anything but gradualist.

As for the convergence argument, I will need more time to read Simon Conway Morris argument in full, however, what it seems to go to, i.e. that convergence disprove contingency, seems to me quite wrong. Once again, my limited understanding of evolutionary theory being stated, I would say that those arguing historical contingency are not arguing that, in a very broad sense, the way life will develop cannot be predicted, but that how it will get there is constrained by history. hence that sometimes less than optimal solution will be adopted because a better one, that might have evolved from an ancestor has been lost and cannot be regained to improve the descent. But yes one can predict that life will try and exploit as many niches as possible in the environment. Mammals, insects and reptile (as birds) all have members that can fly. But the way flight evolved took very different path.
In that sense historical contingency is strong. And every time a new structure/pathway evolve, it will create both new possibilities and new constraints for the future generations of organisms. And those cannot neither be predicted, nor, and I think this is were I diverged with Conway-Morris, be dubbed as insignificant. For example the fact that insects have exoskeleton rather than endoskeleton will forever bring massive constraints as to the size/shape that they will be able to reach because of simple mechanical problems.

So as I see matters the original question of this thread “whether there have been any experiments conducted that provide empirical support for macroevolution.”
As yet no

Lenksi’s experiment is probably the most extensive yet and after over 20years of selective pressure over some 360,000 generations ( 12 x 30,000) has produced a minor novel trait.


As far as I know, once again, the split between macro and micro-evolution is mostly used by ID/creationist rather than biologists who all assume that there is only a continuum (although probably not completely smooth, but certainly not a massive divide). That said, no, there are no controlled experiments that led to massive changes but:
- Think about time scale, doing this kind of experiment is not easy, for one thing funding to run an experiment that long is not exactly easy to secure (why is there only one Lenski? money is an important reason). And bacteria are quite fast at replicating.
- Look at dogs, certainly not a controlled experiment, but over a much reduced (compared to Lenski's bacteria) massive changes in body shapes, abilities and diversity have been selected in many domesticated animals.
- Controlled environment and nature are very different, how do you introduce phages, UV, other bacteria and other very important factors in your experiment? Those are challenges that have for the moment no answers, but they would be valuable.

In conclusion, the simple fact that Lenski has been able to do what he is doing, is wonderful and you should remember that if his bacteria have not evolved one specific trait, on the other hand they have changed a lot as compared to the ancestors, and maybe there are other important changes that have not been noticed in this experiment just because noone has looked at them yet...
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Re: Experimental evidence for evolution

Postby jevg » Mon Jun 28, 2010 2:47 pm

canolan
And as far as I understand it, the historical contingency is definitely a huge part of the evolution as it is now accepted, and was already part of Darwin's understanding, even if he did not emphasize it in the the origin of species. Granted, my lecture of it was probably contaminated by my knowledge of recent biology, but it does not seem that Gould was revolutionary on this respect.

jevg
As canalon has noted, Darwin was aware of this privately but did not try to explain in his “Origin of Species” .His theory was based on gradualism and this gradualism has been retained in the modern synthesis.

canolan
Attention, I did not say that. What I said is that historical contingency was tacit in the Origin of Species, at least when I read it, but certainly not punctuated equilibrium. Which is a definitely new evolution (pun intended) of the theory brought by Gould and Eldridge. I do not think that Darwin was anything but gradualist.




My apologies, I understood from your comment that you were aware of the private note of Darwin that Eldridge drew attention to in an interview as curator Darwin at the American Museum of Natural History.

http://www.amnh.org/exhibitions/darwin/ ... dredge.php

Q: Could you explain what Darwin meant when he wrote, "If species really, after catastrophes, created in showers world over, my theory false"? Did Darwin think of extinction events to be a hindrance to his theory? Was his theory false? Why not?

A: It turns out that the rock record shows that species are very stable—often for millions of years. They don't show a lot of evolutionary change. But his theory's not false. It's just that most evolutionary change occurs in relatively rapid bursts—5 or 50,000 years—rather than millions of years, where they're typically stable.
So his theory's not false—it's just a special form that he wrote that theory. He insisted that it must be slow, steady, gradual change—progressive through time. And when he saw that this wasn't the case, he blamed the fossil record. He said: The fossil record is faulty.
It turns out the fossil record was great, and it shows what happens over millions of years—and very often species remain stable for millions of years. And when evolution then happens, it happens over 50,000 years; 100,000 years. That's rapid geologically—it's not rapid ... too rapid for evolution to occur, though. And natural selection can move and change the adaptations of species in these sudden spurts.

Q: How does your work contradict that? Do species change much over time?

A:Evolution, it turns out, happens—can happen very rapidly. A couple of thousand years is often enough to establish a new species. And this seems to be the norm, rather than the kind of picture that Darwin painted—of slow, steady, gradual change through time. It's just rapid periods of change that interrupt these longer—much longer—periods of relative stability.
What we see in the fossil record is that evolution happens in rapid bursts.”

You are quite correct, Darwin was a gradualist however he did note that the fossil record did not support his theory of gradualism and so put it down to a faulty/incomplete fossil record.

The problem as I see it is that paleontology is an historical science and therefore the data is subject to interpretation depending on the model used. It was in this background that Darwin formulated his theory.

However now we can rely on the science of genetics which of course presents actual data from experimentation. It is here that Darwinian theory is proving unfounded.

I would like to take up your other points shortly.
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Re: Experimental evidence for evolution

Postby jevg » Sat Jul 03, 2010 5:36 pm

A further response to canolan’s last post
As far as I know, once again, the split between macro and micro-evolution is mostly used by ID/creationist rather than biologists who all assume that there is only a continuum (although probably not completely smooth, but certainly not a massive divide)


Actually all biologists do not all assume this continuum as you suggest. In fact for every biologist (Phd) who holds to the view of this micro/macro continuum another can be named who challenges that view
I would encourage you to examine the works of Jim Shapiro and others. Here is a start.
http://shapiro.bsd.uchicago.edu/21st_Ce ... _Evol.html

Look at dogs, certainly not a controlled experiment, but over a much reduced (compared to Lenski's bacteria) massive changes in body shapes, abilities and diversity have been selected in many domesticated animals.


Your example is one of artificial selection not natural selection. A better example would perhaps be wolves and dogs, however in both cases the examples are varieties within the same species. I would argue your example supports the divide between species rather than a continuum.

- Controlled environment and nature are very different, how do you introduce phages, UV, other bacteria and other very important factors in your experiment? Those are challenges that have for the moment no answers, but they would be valuable


I agree with you in the matter of controlled and natural environment being different, however I do not agree that the introduction of phages or UV would impact on the experiment to the degree that one might expect.
May I quote from part of the Shapiro paper cited above.

The conventional view is that genetic change comes from stochastic (random), accidental sources: radiation, chemical, or oxidative damage, chemical instabilities in the DNA, or from inevitable errors in the replication process. However, the fact is that DNA proofreading and repair systems are remarkably effective at removing these non-biological sources of mutation.

For example, consider that the E. coli cell replicates its 4.6 megabase genome every 40 minutes. That is a replication frequency of almost 2 kHz. Yet, due to the action of error-recognition and correction systems in the replication machine and in the cell to catch mistakes in already-replicated DNA, the error rate is reduced below one mistake in every 1010(10 to power 10) base-pairs duplicated, and a similar low value is observed in mammalian cells (32). That is less than one base change in every 2000 cells, certainly well below the mutation frequencies I have measured in E. coli of about four mutations per every 100 to 1000 cells. (my emphasis)

In addition to proofreading systems, cells have a wide variety of repair systems to prevent or correct DNA damage from agents that include superoxides, alkylating chemicals and irradiation (33). Some of these repair systems encode mutator DNA polymerases which are clearly the source of DNA damage-induced mutations and also appear to be the source of so-called "spontaneous" mutations that appear in the absence of an obvious source of DNA damage (34). Results illustrating the effectiveness of cellular systems for genome repair and the essential role of enzymes in mutagenesis emphasize the importance of McClintock’s revolutionary discovery of internal systems generating genome, particularly when an organism has been challenged by a stress affecting genome function.

Darwinian or neo Darwinian theory was for it’s day, however with the advances in our knowledge of cell machinery those ideas really don’t stand the test of experimental evidence.
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Re: Experimental evidence for evolution

Postby jevg » Wed Jul 21, 2010 10:36 am

I would like to add some further evidence to this thread to support the view that the current Darwinian theory is in serious trouble.

Support for the gradualism of the standard theory is definitely declining.
This is most obvious among developmental biologists who are promoting a “New Evolutionary Synthesis”. There is an online book on the National Center for Biotechnology Information website
http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=dbio

You can read this new theory in Chapter 22 “New Evolutionary Synthesis”

Now it is often stated that the human genome contains about 25,000 genes. This actually represents, according to various estimates, from about 2-5% of the total genome. Most of the rest of these are regarded as junk DNA, leftovers from evolutionary process and the bulk of the standard neo Darwinian synthesis concentrates on these 25,000 or so called “coding genes”. These are the ones that code for protein and regarded by Dawkins, for example, as the fundamental unit of evolution, in his “selfish gene” hypothesis.

In the last few years we have learned that over 90% of our genome transcribes into RNA sequences at some development stage in cells and tissue. They form part of an incredibly complex regulatory system.

“The eukaryotic genome as an RNA machine” is the title of a recent paper that discusses this.
http://www.sciencemag.org/cgi/content/a ... /5871/1787

Most, if not close to all, of our chromosomal DNA consists of different types of genes that
have only recently been discovered.
The number in the human genome is now estimated to be 25000 protein coding plus an additional about 450,000+ RNA transcribed genes.
The vast majority of the genome therefore is transcribed, either into protein-coding genes or into regulatory RNA’s.

Some of these RNA gene range in length from only 20 or so genetic letters to millions
of letters long.

In 2004 Francis Collins co authored a paper entitled
“Genome sequence of the Brown Norway rat yields insights into mammalian evolution”
http://www.nature.com/nature/journal/v4 ... 6.html#a56

Have a look at some of the images in this paper, 2 of which are worth a close look (I haven't yet obtained permission to post images direct to this forum)
For ease of reference open the url in a new tab
http://www.nature.com/nature/journal/v4 ... 26_F9.html

Figure 9d of the paper shows the relative densities of SINE’s (Short Interspersed Nuclear Elements) and LINEs (Long Interspersed Nuclear Elements).

Both these elements are types of mobile DNA known as Retrotransposons and together comprise about half of the mammalian genome.
Without worrying too much about the technical details just focus on the relative densities of these elements.
What we have here are the relative densities of LINEs and SINEs along 110,000,000 DNA letters of Rat chromosome 10 (From Fig. 9d of reference 1.)
The x-axis represents the sequence of letters in DNA and the blue line indicates where SINEs occur.
What is clear from the figure, LINEs (pink boxes) tend to peak in abundance where SINEs (blue boxes). taper off and vice versa There is therefore a compartmentalization of LINEs and SINEs in a kind of a bar code structure along the chromosome.

Now the paper then goes on to show the comparison between this density pattern on the Rat as compared with the Mouse chromosome.

Have a look at Fig 9c

The similarity of these two patterns is quite remarkable, as Francis Collins himself notes
“Despite the different fates of SINE families, the number of SINEs inserted after speciation in each lineage is remarkably similar:” (my emphasis)

The problem this evidence poses for Darwinian theory is this.

According to the theory the Mouse and the Rat diverged from each other from the last common ancestor (LCA) i.e. they became separate species. This took place about 20 million years ago (perhaps 12-22 million years).

So a natural question is:-
How could two separate lineages with their separate histories of random mutations (the paper suggests over 300,000 mutations) produce two almost identical patterns.

300,000 random mutation events in the mouse have to somehow match the 300,000 random mutation events in the rat.
Is that a realistic scenario ?

The fact is that these density patterns are highly Non Random.
Incidentally the same pattern occurs in the human genome.

The other fact is that these elements accumulate around the protein coding genes and are clearly now being seen to have a regulatory function.

In the light of all this emerging evidence it comes as no surprise that development biologists are openly questioning the standard dogma.

There is a lot more evidence but this I am sure is sufficient for the moment.
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Re: Experimental evidence for evolution

Postby TheSymphofBiology » Wed Jul 21, 2010 11:57 pm

jevg wrote:I would like to add some further evidence to this thread to support the view that the current Darwinian theory is in serious trouble.


This is something I've heard ID/Creationists say countless times.
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